Exactly! A ninja will be found only if he wants to be, at least a good one. If my boyfriend woke up and saw that, he'd laugh his ass off because he loves ninjas. The question I have, what was the Original Poster being pointed at with? A gun? A sword? A stick? A pointer finger? I wish OP would have wrote which weapon was the ninja's choice.

I think you should freak him out, open the window the next morning in a clown outfit. The next day open it up drenched in blood and a look of total surprise that someone saw you committing heinous acts of violence. Keep doing this till he no longer feels comfortable coming back lol

Operator, "9-1-1, please state your emergency." OP, "Yeah, um, there's a ninja on a roof next to me and is pointing something at me. Send help immediately; I'm scared for my life!" Operator, "Okay, we will send a police officer when one is available. I can't guarantee a time because this doesn't sound like an emergency." OP, "Fuck you! I said I'm scared for my life."...I'm guessing that's how the conversation took place, which sounds epic! haha

It's hard to find a ninja when they get out of the costume when they're done.
Depending on how hard it is to get onto the neighbor's roof, the neighbor may be the only option. In which case it's someone OP knows, and probably shouldn't be worried about.
Though, if OP is bothered enough, no ninja can run and hide with a sniper bullet lodged in their forehead.